Package: surimi 1.0.0.0

Bruce Delo

surimi: Convert Acoustic Telemetry Data Between Institutional Formats

Surimi takes as input data files representing acoustic telemetry, which may have column names and structures specific to particular institutions. It can convert, with minimal code on the user's part, data from one format to another, allowing data from one institution to be easily used across software packages that may expect different formats.

Authors:Bruce Delo [aut, ctb, cre]

surimi_1.0.0.0.tar.gz
surimi_1.0.0.0.zip(r-4.7)surimi_1.0.0.0.zip(r-4.6)surimi_1.0.0.0.zip(r-4.5)
surimi_1.0.0.0.tgz(r-4.6-any)surimi_1.0.0.0.tgz(r-4.5-any)
surimi_1.0.0.0.tar.gz(r-4.7-any)surimi_1.0.0.0.tar.gz(r-4.6-any)
surimi_1.0.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
surimi/json (API)

# Install 'surimi' in R:

install.packages('surimi', repos = c('https://ocean-tracking-network.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ocean-tracking-network/surimi/issues

On CRAN:

3.52 score 6 stars 4 scripts 12 exports 63 dependencies

Last updated from:8638e69074. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	127
source / vignettes	OK	191
linux-release-x86_64	ERROR	145
macos-release-arm64	ERROR	94
macos-oldrel-arm64	ERROR	103
windows-devel	ERROR	62
windows-release	ERROR	62
windows-oldrel	ERROR	59
wasm-release	OK	134

Exports:glatos_to_ato glatos_workbook_to_ato imos_otn_column_map imos_to_otn_detections imos_to_otn_receivers imos_to_otn_tags load_file map_otn_file otn_imos_column_map otn_imos_new_style_column_map otn_to_ato rollup

Dependencies:av cellranger class classInt cli cpp11 crayon crul curl data.table DBI dplyr e1071 gdistance generics geodist glatos glue hms httpcode igraph jsonlite KernSmooth lattice lifecycle lubridate magrittr MASS Matrix mime nanoparquet pillar pkgconfig plotrix prettyunits progress proxy purrr R6 raster Rcpp readxl rematch rlang s2 sf sp stringi stringr terra tibble tidyr tidyselect timechange triebeard units urltools utf8 vctrs withr wk worrms zip

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Consult a lookup table for the aphiaID.	get_aphiaid_from_lookup
Get AphiaIDs for scientific names	get_unique_aphiaids
Convert GLATOS detection data to an ATO object.	glatos_to_ato
Convert GLATOS workbook to an ATO object.	glatos_workbook_to_ato
Map IMOS receiver metadata to an OTN-like format	imos_otn_column_map
Map IMOS detection data to an OTN-like format	imos_to_otn_detections
Map IMOS receiver metadata to an OTN-like format	imos_to_otn_receivers
Map IMOS tag metadata to an OTN-like format	imos_to_otn_tags
Load a detection extract of either parquet, Excel or CSV format.	load_file
Determine whether an input file is CSV or Parquet and pipe it into the correct mapping function. Hopefully this is all a stopgap until the typical format of OTN -> ATO and then ATO -> IMOS gets done, at which point those pipeline pieces will connect together. But for now, this will keep dependent software like Remora running.	map_otn_file
Map OTN-formatted data to IMOS-format	otn_imos_column_map
Map OTN-formatted data from our new Parquet detection extracts to IMOS-format	otn_imos_new_style_column_map
Convert OTN detection data to an ATO object.	otn_to_ato
Join output from Remora back onto its OTN detection extract.	rollup